BEIRUT — The moderate rebel command at the center of U.S. policy in Syria is becoming increasingly marginalized as dozens of militias peel away to form rival, Islamist alliances in a move that could leave the Obama administration with no battlefield partner in the fight to topple President Bashar Assad.

The Supreme Military Command and its forces, known collectively as the Free Syrian Army, are reeling as 40 or more affiliates this month have signed onto two new umbrella groups, both with agendas that are at odds with the U.S.-backed opposition’s long-stated vision of a democratic, pluralistic Syria.

If the project to build rival Islamist commands succeeds, opposition activists and Middle East analysts warn, the Supreme Military Command is likely to fizzle quickly, essentially ending talk of a “moderate” rebel force to counter the influence of Islamist insurgents, including at least two factions aligned with al Qaida.

“Because we’re short on ammunition, short on supplies, some of our groups are going to them. The Islamists have their own supplies,” said Louay Meqdad, a spokesman for the Free Syrian Army. “We’re asking the international community: Please don’t leave our people to choose between joining the extremists and surrendering to Bashar Assad.”

The two emerging Islamist umbrella groups are known as the Azzaz Declaration Signatories in the north and, in the capital, Damascus, as the Army of Islam. Though both groups are nascent, their arrival hardens the conflict’s turn from an anti-authoritarian rebellion to a Sunni Muslim campaign to overthrow a regime led by the minority Alawite sect and replace it with a government “consistent with the principles of Islamic law.”

That’s a far cry from the U.S.-backed opposition’s vision of a secular democracy with protection of minority rights.

Meqdad said the force behind the formation of the Army of Islam, Zahran Alloush, a founder of the Liwa al Islam militia who’d been part of the Supreme Military Command, personally assured him that this was just a “gathering” of groups under an Islamist banner. Alloush’s father reportedly is a Salafist cleric in Riyadh, Saudi Arabia, and the family is said to have Saudi backing, fueling rumors that the new project is Saudi Arabia lashing out at U.S. policy by creating a parallel command to mount a more serious fight against Assad.

Meqdad rejected the idea that Persian Gulf powers were behind the alliance but stressed that Alloush owed his rebel comrades an explanation.

“For sure, we are not happy about anyone starting his own army,” Meqdad said. “This is not the time for this. We can’t divide the cake before we even get it.”

Meqdad said internal talks are to be held within days to figure out exactly which brigades are leaving the Free Syrian Army and whether to expect the new Islamist groupings to cooperate in battle or whether the goal is really to sideline the Supreme Military Command and its leader, Gen. Salim Idriss.

Officials said Idriss heard reassurances over the weekend from Ambassador Robert Ford, the State Department’s envoy to the Syrian opposition, that the Obama administration would keep supporting and delivering aid to the command. The two met in Istanbul, the Turkish city that’s a hub for opposition organizing.

But how Ford’s pledge could be fulfilled is unclear, with growing difficulties in getting equipment to the moderates now that al Qaida-aligned groups control key border crossings and with increasing number of rebel units publicly disavowing any connection to the Supreme Military Command.

Fighters and observers of the conflict say the chief motivations for the shift away from the Supreme Military Command are frustration with the U.S. government’s slow delivery of promised combat equipment and President Barack Obama’s decision not to launch missile strikes against the Assad regime in retaliation for a deadly chemical weapons attack.

Another main issue was the attempted takeover of the rebel movement by al Qaida’s Syria branch, the Islamic State of Iraq and Sham, better known by the acronym ISIS. Most of the rebel groups, even fellow Islamists, decry that group’s extremist ideology and merciless dealings with local communities.

ISIS has been engaged in fierce gunfights with more moderate rebels, who out of concern that the Supreme Military Command isn’t up to the fight are turning to the other al Qaida affiliate in the Syrian conflict, Jabhat al Nusra, also known as the Nusra Front. Despite its U.S. designation as a terrorist organization, many now consider Nusra closer to the mainstream because of its own rivalries with ISIS.

“In comparison to ISIS – the Syria Iraq al Qaida group – al Nusra, well, they look moderate,” Kristalina Georgieva, the European Union’s commissioner for international coordination, humanitarian aid and crisis response, said Friday at a Syria talk at the New America Foundation in Washington.

In addition, there was festering disdain for the Syrian Opposition Council, the political opposition that, ostensibly at least, oversees the Supreme Military Command. The political opposition members are derided as exiles and “hotel revolutionaries,” though until now there had been higher regard for Idriss and his men because of their service in combat.

But now, the Supreme Military Command, too, is fast becoming irrelevant, along with its dream of a moderate, professional force that abides by international norms on human rights and rules of war.

“Now, more than ever, the United States can get behind the SMC to prevent this from taking hold,” Dan Layman, spokesman for the Washington-based Syrian Support Group, a pro-rebel fundraising group, said of the new Islamist alliances. “At the end of the day it’s going to be about supplies: Who can support the fighters?”

Aymenn al Tamimi, a fellow with the Middle East Forum, a conservative research center in Philadelphia, and a monitor of jihadist activity in Syria and Iraq, said that Idriss and his command were good at making pledges but couldn’t back up their words because of a lack of resources.

“I think Idriss had some sway over certain rebel groups in the Damascus area and points south, but a lot of his gestures of being in touch with forces on the ground were only superficially impressive,” Tamimi said.

For example, Tamimi said, Idriss paid a visit to the coastal area of Latakia in a time of fighting, prompting some rebels to rejoice in what they perceived as the Free Syrian Army’s advance.

“On the contrary, as my own research on both sides shows, the Latakia offensive was primarily led by battalions of foreign fighters, and the sole purpose of it was to score a symbolic victory through ethnic cleansing of Alawites,” Tamimi said.

That offensive was the subject of a scathing Human Rights Watch report on Friday that accused the rebels, led by ISIS, Nusra and three other groups, of killing scores of civilians and kidnapping at least 200 more who are still being held hostage.

The report said it had no evidence that troops reporting to Idriss had had a direct hand in the atrocities. But it said Idriss’ assertion that Supreme Military Command-allied units had taken part in the offensive should be examined, and it urged the Supreme Military Command to cease any cooperation with the Islamist groups.

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